1TGZ

Structure of human Senp2 in complex with SUMO-1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex

Reverter, D., Lima, C.D.

(2004) Structure 12: 1519-1531

  • DOI: 10.1016/j.str.2004.05.023
  • Primary Citation of Related Structures:  
    1TGZ, 1TH0

  • PubMed Abstract: 

    • Modification of cellular proteins by the ubiquitin-like protein SUMO is essential for nuclear metabolism and cell cycle progression in yeast. X-ray structures of the human Senp2 catalytic protease domain and of a covalent thiohemiacetal transition-state complex obtained between the Senp2 catalytic domain and SUMO-1 revealed details of the respective protease and substrate surfaces utilized in interactions between these two proteins ...

    Modification of cellular proteins by the ubiquitin-like protein SUMO is essential for nuclear metabolism and cell cycle progression in yeast. X-ray structures of the human Senp2 catalytic protease domain and of a covalent thiohemiacetal transition-state complex obtained between the Senp2 catalytic domain and SUMO-1 revealed details of the respective protease and substrate surfaces utilized in interactions between these two proteins. Comparative biochemical and structural analysis between Senp2 and the yeast SUMO protease Ulp1 revealed differential abilities to process SUMO-1, SUMO-2, and SUMO-3 in maturation and deconjugation reactions. Further biochemical characterization of the three SUMO isoforms into which an additional Gly-Gly di-peptide was inserted, or whereby the respective SUMO tails from the three isoforms were swapped, suggests a strict dependence for SUMO isopeptidase activity on residues C-terminal to the conserved Gly-Gly motif and preferred cleavage site for SUMO proteases.

    Organizational Affiliation: 

    Structural Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sentrin-specific protease 2A226Homo sapiensMutation(s): 0 
Gene Names: SENP2, KIAA1331
EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC62 (Homo sapiens)
Explore Q9HC62 
Go to UniProtKB:  Q9HC62
PHAROS:  Q9HC62
GTEx:  ENSG00000163904 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HC62
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3CB80Homo sapiensMutation(s): 0 
Gene Names: UBL1, SMT3H3, SMT3C, SUMO1, OK/SW-cl.43
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
PHAROS:  P63165
GTEx:  ENSG00000116030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63165
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.163α = 90
b = 111.163β = 90
c = 143.106γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance